Variant report

Variant	rs2549063
Chromosome Location	chr16:74566474-74566475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11641958	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12598701	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12716768	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12927939	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13339161	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13339456	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13380609	0.81[ASN][1000 genomes]
rs1469140	0.81[AMR][1000 genomes]
rs1971071	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2303281	0.83[AMR][1000 genomes]
rs2549559	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2550816	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2868035	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28762730	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3096409	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3865164	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3960602	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3973385	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4404098	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4887772	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7188050	0.88[AMR][1000 genomes]
rs7189123	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7190577	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7195020	0.86[AMR][1000 genomes]
rs7195196	0.89[AMR][1000 genomes]
rs7195198	0.89[AMR][1000 genomes]
rs8045653	0.89[AMR][1000 genomes]
rs9923616	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948443	chr16:73994997-74627711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1065964	chr16:74088091-74575604	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
4	esv2758431	chr16:74334780-74587185	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2758656	chr16:74334780-74587185	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv428806	chr16:74394226-74580125	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv833278	chr16:74415944-74584123	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv1060629	chr16:74483574-74660669	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv833279	chr16:74490746-74663073	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
13	nsv906905	chr16:74527618-74679244	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2549063	MLKL	Cis_1M	lymphoblastoid	RTeQTL
rs2549063	RFWD3	cis	Esophagus Mucosa	GTEx
rs2549063	RFWD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74525400-74572200	Weak transcription	HUVEC	blood vessel
2	chr16:74537400-74567000	Weak transcription	Colon Smooth Muscle	Colon
3	chr16:74537600-74568600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr16:74537600-74579800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr16:74537600-74604800	Weak transcription	Thymus	Thymus
6	chr16:74537800-74568800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr16:74538000-74567000	Weak transcription	HMEC	breast
8	chr16:74539200-74578200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr16:74539200-74581600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr16:74540000-74579800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr16:74542600-74567400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr16:74542600-74574800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr16:74542800-74566800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:74542800-74590400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr16:74543000-74567000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr16:74543000-74568000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr16:74543000-74570400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:74552200-74575400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr16:74552600-74580000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr16:74555000-74582200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr16:74556000-74567600	Weak transcription	Fetal Muscle Leg	muscle
22	chr16:74556000-74572400	Weak transcription	Brain Angular Gyrus	brain
23	chr16:74556200-74568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr16:74556400-74567000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr16:74556400-74568600	Weak transcription	Brain Anterior Caudate	brain
26	chr16:74556400-74572400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr16:74556400-74595600	Weak transcription	NH-A	brain
28	chr16:74556800-74567000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr16:74556800-74567400	Weak transcription	Left Ventricle	heart
30	chr16:74556800-74568800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:74556800-74568800	Weak transcription	Brain Substantia Nigra	brain
32	chr16:74558400-74568800	Weak transcription	Psoas Muscle	Psoas
33	chr16:74558800-74567400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr16:74558800-74578200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr16:74559000-74574600	Weak transcription	HepG2	liver
36	chr16:74559200-74566600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr16:74559200-74567600	Weak transcription	Primary B cells from cord blood	blood
38	chr16:74559200-74568600	Weak transcription	Osteobl	bone
39	chr16:74559200-74572400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr16:74559200-74594000	Weak transcription	Ovary	ovary
41	chr16:74559400-74566600	Weak transcription	Fetal Lung	lung
42	chr16:74559400-74567000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr16:74559400-74567000	Weak transcription	Fetal Intestine Large	intestine
44	chr16:74559400-74567800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr16:74559400-74567800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr16:74559400-74568000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr16:74559400-74568200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr16:74559400-74568200	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr16:74559400-74569000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr16:74559400-74569600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links